d963cff5bbdcbfd55650c774a3ccf441 pmc_33019720.pdf badf9442b55357df0c19fd83902f65e434911e17 pmc_33019720.pdf f8b029899852bcbc18f2bc16d8c19266b4426e71305084e3f9293f64929881b0 pmc_33019720.pdf Title: Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples Subject: Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks. Keywords: lncRNAs enrichment; CRC; FFPE samples Author: Susana Iraola-Guzmán, Anna Brunet-Vega, Cinta Pegueroles, Ester Saus, Hrant Hovhannisyan, Alex Casalots, Carles Pericay and Toni Gabaldón Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Tue Oct 13 03:24:49 2020 CEST ModDate: Tue Oct 13 03:56:38 2020 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 20 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 3966782 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- USXBDB+Pxsy Type 1 Builtin yes yes no 10 0 OHKNFJ+VnURWPalladioL Type 1 Custom yes yes no 14 0 IKMUEY+URWPalladioL-Ital Type 1 Custom yes yes no 19 0 UICKUM+URWPalladioL-Bold Type 1 Custom yes yes no 24 0 RCFYRP+Rpxb Type 1 Builtin yes yes no 28 0 FJPIBA+URWPalladioL-Roma Type 1 Custom yes yes no 32 0 OFLXAT+Rpxr Type 1 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Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Results and Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Design of a lncRNA-Focused Enrichment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Validation of Probe-Based Enrichment of lncRNAs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Identification of Differentially Expressed lncRNAs in CRC Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Validation of Gene Expression Data of a Subset of DE lncRNAs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Identification of CRC-Related Somatic Mutations in FFPE Samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Material and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Children: Item: Title: Ethics Statement Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Patients and Samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: RNA Isolation From FFPE, FF, and Cell Line Cultures Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Custom Design of Probes for lncRNA Enrichment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Library Preparation, lncRNA Enrichment and Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Quality Control, Pseudo-Mapping and Gene Abundance Quantification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Differential Expression Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Gene Expression Quantification of TCGA Samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Characterization of Differentially-Expressed lncRNAs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: SNP Calling Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Validation of lncRNA Expression by Real-Time Quantitative PCR (RT-qPCR) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Info: Title: Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples Author: Susana Iraola-Guzmán, Anna Brunet-Vega, Cinta Pegueroles, Ester Saus, Hrant Hovhannisyan, Alex Casalots, Carles Pericay and Toni Gabaldón Subject: Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks. 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Link Rect: 279, 354, 315, 364 Annotation: Subtype: Link Rect: 452, 327, 490, 338 Annotation: Subtype: Link Rect: 294, 302, 331, 312 Annotation: Subtype: Link Rect: 76, 260, 166, 291 Annotation: Subtype: Link Rect: 234, 254, 407, 265 Checksum: 1a48a4f9 Type: CRC32 Checksum: d963cff5bbdcbfd55650c774a3ccf441 Type: MD5 Checksum: badf9442b55357df0c19fd83902f65e434911e17 Type: SHA-1